Snake Meat......source of chinese virus

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Early on in this thread, we pointed to the ethnic link to varying amounts of ACE2 receptors relative to COVID-19 susceptibility. Recently, another ACE2 factor has come to light.

COVID-19 Glycosylation / Chloroquine

Hyperglycemia, hydroxychloroquine, and the COVID-19 pandemic - PubMed

Coronavirus disease-2019 (COVID-19) infection and its severity can be explained by the concentration of glycosylated severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) viral particles in the lung epithelium, the concentration of glycosylated angiotensin-converting enzyme receptor 2...

www.ncbi.nlm.nih.gov

'Hyperglycemia, Hydroxychloroquine, and the COVID-19 Pandemic....It allows consideration of agents, such as hydroxychloroquine, which may interfere with this brisk macrophage inflammatory response....

Comment on Hyperglycemia, Hydroxychloroquine, and the COVID-19 Pandemic the hyperglycemia at the admission in the hospital
'Hyperglycemia and the Worse Prognosis of COVID-19. Why a Fast Blood Glucose Control Should Be Mandatory....in particular those that blunt but do not completely abrogate the M1 to M2 balance in macrophage polarization, as well as viral load, which in SARS appears to be temporally related to the onset of ARDS....particularly the hyperglycemia at the admission in the hospital is a very bad prognostic factor. 1. an acute increase of glycemia is accompanied by a huge increase in inflammatory mediators. 2. another reason seems to be very specific for COVID-19 and it is related to the binding of SARS-CoV-2 to ACE2. The glycosylation, a reaction that can be induced by hyperglycemia, of the ACE2, is needed for the linkage of the virus to this cellular receptor. It is the amount of glycosylated ACE2 receptor, and not simply the amount of ACE2 alone that is responsible for the virus binding and fusion.'

 

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Thus the contraindications due to hydroxychloroquine depend on the glycosylation profile of each patient, for example, hypoglycemics vs diabetics.

 

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The embarassing history of the search for ebola virus vectors and reservoirs in nature may be end up a replay for COVID-19. Nonetheless, a vaccine did emerge. It is based on a virus of cattle, vesicular stomatitis virus (VSV). One COVID-19 link is here:

Dexamethasone / VSV

Ras (proto)oncogene induces N-linked carbohydrate modification: temporal relationship with induction of invasive potential - PubMed

The effect of expression of the ras oncogene on protein glycosylation was studied. VSV G-protein and class I histocompatibility antigens were analysed to monitor ras-mediated changes in glycosylation. Transient expression of the c-Ha-ras oncogene, introduced into NIH 3T3 cells by the...

www.ncbi.nlm.nih.gov

Computers and Viral Disease

Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus - PubMed

This paper concerns study of the genome of the Wuhan Seafood Market isolate believed to represent the causative agent of the disease COVID-19. This is to find a short section or sections of viral protein sequence suitable for preliminary design proposal for a peptide synthetic vaccine and a...

www.ncbi.nlm.nih.gov

'....This paper concerns study of the genome of the Wuhan Seafood Market isolate believed to represent the causative agent of the disease, COVID-19. This is to find a short section or sections of viral protein sequence suitable for preliminary design proposal for a peptide synthetic vaccine and peptidomimetic therapeutic, and to explore some design possibilities....KRSFIEDLLFNKV was found to be particularly well conserved in this study and corresponds to the region around one of the known cleavage sites of the SARS virus that are believed to be required for virus activation for cell entry....Preliminary studies using molecular modeling and docking, and in that context the potential value of certain herbal extracts, are also described.'

The sequence, KRSFIEDLLFNKV, can be musically represented for piano, etc. according to the amino acid protocol in post #2 of the Evolution of the Saxophone thread.

 

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The following can not only be musically represented, it is an example of the protocol for COVID-19 vaccine design, as the article 'Computers and Viral Diseases' continues:

Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus - PubMed

This paper concerns study of the genome of the Wuhan Seafood Market isolate believed to represent the causative agent of the disease COVID-19. This is to find a short section or sections of viral protein sequence suitable for preliminary design proposal for a peptide synthetic vaccine and a...

www.ncbi.nlm.nih.gov

'....First recall the sequence in the Wuhan seafood market isolate: FGGFNFSQILPDPSKPS(KRSFIEDLLFNKV)TLADAFGFIKQYGDC

To compare, an alternative to the part in brackets is RSFIDELAFGRG.
It is an example of a tentative (specific [italics]) design "hunch" based on a section of a human semaphorin (GenBank NP_001243276) produced in response to lung diseases, a suggestive biologically-related match with conservative replacements but (not [it.]) one suggested by the (general [it.]) rules and probably coincidental.

In the first peptide suitable as a candidate for a peptide vaccine, the principles, once given the core KRSFIEDLLFNKV sequence motif, are as follows. This is to add a C-terminal cysteine (C) as a linkage (other chemical linkages are certainly [possible) to the carrier connected by a moderately flexible TLA (threonine-leucine-alanine) arm. This is found at the same locus and conservatively retained. The sequence is specifically after LA because the -(COO-) terminus of the protein will mimic the aspartate (D) found in that position in the original sequence (but not, accordingly, in the peptide modeling the epitope).'

 

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Promedmail has just recorded a VSV outbreak: 19 Jun 2020 'The Kansas Department of Agriculture (KDA) has announced that vesicular stomatitis virus (VSV) was confirmed in horses in Butler County on 16 Jun 2020. Kansas becomes the fourth US state to have confirmed cases of VSV this year. The infected horses lived on different private residences in south central Kansas.

Computers and Viral Diseases
'....The rationale is that the section KRSFIEDLLFNKV is exposed as associated with S2' at the surface but highly conserved as shown in the second (i.e. "FIEDLL") alignment. To bring it to the length circa 20 amino acid residues considered in the author's experience (and frequently by other workers) as most suitable as a basis of B-epitope for vaccine and diagnostic design, it was noted that the preceding serine (S) and following leucine (L) and alanine (A) are found in 29019 nCoV, well conserved in human host (AAR07628.1) and bat host species and represent fairly conservative substitutions in the next most related coronavirus, the pig host species....A carrier protein is required to be added for antibody production and the system memory because short peptides have limited antigenicity.'

 

[badger2]

The New York Times has an important salmon update, revealing a previous political salmon event:

NYT 19 Jun 2020 Coronavirus Fears in China Find a New Target: Salmon

Coronavirus Fears in China Find a New Target: Salmon

When a new coronavirus outbreak emerged last week in Beijing, residents were jolted by reports that traces of the virus had been found on a cutting board used for imported salmon, and the backlash was swift.Within a few days, salmon was removed from major supermarket shelves in Beijing, reserves...

news.yahoo.com

 

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Two vaccine trials begin in Russia:
21 Jun 2020 Moscow Times, Coronavirus in Russia: The Latest News

Coronavirus in Russia: The Latest News | Feb. 24 - The Moscow Times

Russia has confirmed 18,315,292 cases of coronavirus and 378,784 deaths, according to the national coronavirus information center. Russia’s total excess fatality count since the start of the coronavirus pandemic is at least 995,000. Under half the population is fully vaccinated.

themoscowtimes.com

'....a special disinfection tunnel has been installed at President Vladimir Putin's residence outside Moscow....The Russian military has started testing a coronavirus vaccine on 18 volunteers. On Wednesday, the Health Ministry said its coronavirus vaccine trials had begun with two groups of 38 volunteers.'

 

[badger2]

This report leaves questions unanswered about viral subsistence on surfaces.

18 Jun 2020 Coronavirus Beijing: Why an Outbreak Sparked a Salmon Panic in China
bbc.com/news/world-asia-china-53089137
'....But 40 samples from the market tested positive for the virus -- some of which were not from chopping boards used to cut salmon....There was no trace of the virus on salmon before it reached the market -- suggesting that the virus was present in the market, rather than in the salmon itself. And experts agree.....Coronaviruses cannot multiply in food; they need an animal or human host to multiply.'

This reasoning is misleading. We have already shown the German coronavirus study in this thread that reveals a porcine coronavirus that can subsist on steel surfaces for up to 24 days.

1.) What are the details of the 40 samples relating to surfaces? From what surfaces were the samples taken?

2.) How long can COVID-19 subsist on various surfaces, and at what temperatures and humidities?

3.) How was it established that there was no trace of COVID-19 on the salmon before it reached the market?

4.) The scientific community is suspicious of the claim of "European" markers in the sample. Apart from heresay, where is the evidence of a European strain?

 

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Post #391 shows up to 28 days on steel for TGEV and MHV (murine hepatitis [corona]virus). The virus does not need a host to be infective.

usmessageboard.com/threads/snake-meat-source-of-chinese-virus.802608/page-20#post-24048373

We thus refer back to isopeptidase mentioned earlier in the thread and its link to (mouse) murine hepatitis virus (MHV):

MHV / Isopeptidase

X-ray Structural and Functional Studies of the Three Tandemly Linked Domains of Non-structural Protein 3 (nsp3) from Murine Hepatitis Virus Reveal Conserved Functions - PubMed

Murine hepatitis virus (MHV) has long served as a model system for the study of coronaviruses. Non-structural protein 3 (nsp3) is the largest nsp in the coronavirus genome, and it contains multiple functional domains that are required for coronavirus replication. Despite the numerous functional...

www.ncbi.nlm.nih.gov

 

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MHV / Isopeptidase

X-ray Structural and Functional Studies of the Three Tandemly Linked Domains of Non-structural Protein 3 (nsp3) from Murine Hepatitis Virus Reveal Conserved Functions - PubMed

Murine hepatitis virus (MHV) has long served as a model system for the study of coronaviruses. Non-structural protein 3 (nsp3) is the largest nsp in the coronavirus genome, and it contains multiple functional domains that are required for coronavirus replication. Despite the numerous functional...

www.ncbi.nlm.nih.gov

'....The PLP2 catalytic domain was found to have both deubiquitinating and deISGylating (interferon-stimulated gene 15, a ubiquitin-like molecule) isopeptidase activity. CoVs may employ DUB and deISGylating activities of PLPs to antagonize host innate immune responses to infection. Indeed, both SARS CoV Plpro and HCoV-NL63 PLP2 have been shown to interfere with the IRF3 and NF-kappaB signaling pathways for interferon production....The structure of PLP2 and the model of PLP2-Ub complex enables the use of MHV as a model to study the mechanism of coronavirus immune evasion.'

 

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Human hepatitis B virus (HBV) physically attaches to NF-kappaB, and here we also link heron hepatitis virus HHV) to another virus of herons, Nodamura virus:

Nodamura Virus / Oncolytic Vesicular Stomatitis Virus / RNA Interference / Interferon Pathway

https://www.ncbi.nlm.nih/pubmed/29921327

Infectivity for 28 days on steel surfaces for MHV is remarkable, and its biology links to SARS-CoV, both pointing to the possibility of COVID-19 remaining infective on surfaces for longer than suspected.

 

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Note that vsv, of which there was an outbreak in horses in Kansas on 16 Jun 2020, is not only the basis of an ebola vaccine, but is of the family Rhabdoviridae, of which rabiesvirus is a member.

Nodamura Virus / Oncolytic VSV / RNA Interference / Interferon Pathway

Enhanced susceptibility of cancer cells to oncolytic rhabdo-virotherapy by expression of Nodamura virus protein B2 as a suppressor of RNA interference - PubMed

Antiviral responses are barriers that must be overcome for efficacy of oncolytic virotherapy. In mammalian cells, antiviral responses involve the interferon pathway, a protein-signaling cascade that alerts the immune system and limits virus propagation. Tumour-specific defects in interferon...

www.ncbi.nlm.nih.gov

For those studying the media for chloroquine/hydroxychloroquine, recall that we posted the link between chloroquine and bungarotoxin on 10 Feb 2020 in this thread.

1988, U.S. Army Medical Research, Frederick, Md.

Effect of chloroquine on toxicity in mice of the venom and neurotoxins from the snake Bungarus multicinctus - PubMed

Antivenoms are the currently available agents for treatment of snake venom intoxication. The development of therapeutic strategies employing more generally available drugs could improve treatment of invenomation by reducing hypersensitivity reactions, cost and storage requirements. I report that...

www.ncbi.nlm.nih.gov

 

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Post #630 mentions NSP3 (non-structural protein 3) of MHV. In comparison, we point to post #341 as the mutations coalesce:

RBD / ACE2 / NSP1 (Los Angeles, Beijing, Changsha, Souzhou)

Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China - PubMed

An in-depth annotation of the newly discovered coronavirus (2019-nCoV) genome has revealed differences between 2019-nCoV and severe acute respiratory syndrome (SARS) or SARS-like coronaviruses. A systematic comparison identified 380 amino acid substitutions between these coronaviruses, which may...

www.ncbi.nlm.nih.gov

'....No amino acid substitutions were present in the RBM (receptor binding motifs) that directly interact with human receptor for ACE2 S ----protein in SARS-CoV, but six mutations occurred in the other region of the RBD (receptor binding domain). Whether these differences could affect the host tropism and transmission property of 2019-nCoV compared to SARS-CoV is worthy of further investigation....NSP1 at position 269 S ---->L.'

The non-structural protein 3 of murine hepatitis virus (post#630):

X-ray Structural and Functional Studies of the Three Tandemly Linked Domains of Non-structural Protein 3 (nsp3) from Murine Hepatitis Virus Reveal Conserved Functions - PubMed

Murine hepatitis virus (MHV) has long served as a model system for the study of coronaviruses. Non-structural protein 3 (nsp3) is the largest nsp in the coronavirus genome, and it contains multiple functional domains that are required for coronavirus replication. Despite the numerous functional...

www.ncbi.nlm.nih.gov

Another serine-to-leucine is shown by the authors in post #313 in the COVID-19 hypervariable hotspot of ORF8 (open reading frame 8): S ---->L.

We thus think that serine-to-leucine is an important and common phenomenon between SARS-CoV, MHV and COVID-19.

 

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Here are the four refs from Pubmed for Legionnaire's and coronavirus, in chronological order:

Healthcare-associated atypical pneumonia - PubMed

Atypical pneumonia was first described in 1938, and over time, Mycoplasma, Legionella, and Chlamydophila were the agents commonly linked with community-associated atypical pneumonia. However, as technology has improved, so has our understanding of this clinical entity. It is now known that there...

www.ncbi.nlm.nih.gov

SARS-CoV-2 and Legionella co-infection in a person returning from a Nile cruise - PubMed

We report a case of severe acute respiratory syndrome coronavirus 2 and <i>Legionella</i> co-infection manifesting as pneumonia with gastrointestinal symptoms. The case highlights the importance of differential diagnosis during the COVID-19 pandemic, so we do not miss the opportunity to diagnose...

www.ncbi.nlm.nih.gov

[Atypical pathogens of pneumonia acquired in ambulant persons] - PubMed

[Atypical pathogens of pneumonia acquired in ambulant persons]

www.ncbi.nlm.nih.gov

Detection of respiratory viruses and Legionella spp. by real-time polymerase chain reaction in patients with community acquired pneumonia - PubMed

We conducted a study on throat swabs obtained from a group of hospitalized patients with community acquired pneumonia (CAP). Throat swab specimens from 242 adults admitted to hospital with CAP were tested. In total, 1 or more aetiological agents were identified by real-time PCR in 55 (23%)...

www.ncbi.nlm.nih.gov

 

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This report deciphers pangolins' role in COVID-19:

19 Jun 2020 Sunda Pangolins

No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia

The legal and illegal trade in wildlife for food, medicine and other products is a globally significant threat to biodiversity that is also responsible for the emergence of pathogens that threaten human and livestock health and our global economy. Trade in wildlife likely played a role in the...

www.biorxiv.org

'....the lack of any 'upstream' market chain samples suggests that these detections in 'downstream' animals more plausibly reflect exposures to infected humans, wildlife or other animals within the wildlife trade network.'

 

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A COVID-19 nurse sends a note from the front lines:
Avian Flu Talk

From the Frontlines

Gretchen “Awesome People Wear Masks” Winter, MDMay 24Well, friends, today was my last shift...

avianflutalk.com

 

[badger2]

Here is a stat for COVID-19 in water, reflecting our previous post for MHV coronavirus survival on steel surfaces for up to 24 days:

Risk of SARS-CoV-2 infection from contaminated water systems

Following the outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV-2) in China, airborne water droplets (aerosols) have been identified as the main transmission route, although other transmission routes are likely to exist. We quantify SARS-CoV-2 virus survivability within water...

www.medrxiv.org

'....the virus can remain stable in water for up to 25 days....faecal contamination of rivers, waterways, and water systems within countries with high infection rates can provide infectious doses > 100 copies/100 ml of water.'

 

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Mink are capable of infection with COVID-19:

22 Jun 2020 Danish Ministry of the Environment and Food, Notice of COVID-19 in Fur Animals

BEK nr 926 af 22/06/2020, Ministeriet for Fødevarer, Landbrug og Fiskeri

Bekendtgørelse om COVID-19 hos pelsdyr

www.retsinformation.dk

' Formalet med denne bekendtgoerelse er at sikre at Foedevarestyrelsen I forbindelse udtage prover og overvage udbredelsen af COVID-19 I pelsdyr og indfore smittedforebyggende foranstaltninger.
Anyone who, in his custody, has fur animals where one or more of the fur animals can be suspected of being infected with COVID-19 shall call a veterinarian.'

 

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This strategy repurposes a vaccine against COVID-19:

25 Jun 2020 Decades Old Soviet Studies Hint at Coronavirus Strategy

Decades-Old Soviet Studies Hint at Coronavirus Strategy

MOSCOW -- To the boys, it was just a sugary treat. To their parents, prominent medical researchers, what happened in their Moscow apartment that day in 1959 was a vital experiment with countless lives at stake -- and their own children as guinea pigs."We formed a kind of line," Dr. Peter Chumakov

www.yahoo.com

'....Dr. Robert Gallo....to test the effectiveness of live polio vaccine against coronavirus using health care workers as subjects.'

 

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Moscow Times
'Preparat na osnove favipiravir kompanii "Promomed" areplivir dlia lecheniia infektsii
A preparation based on favipiravir by a "promomed" company, areplivir for treatment of COVID-19 infection'

One minute ago

Use of Areplivir Approved by Russian Ministry of Health

Russian Health Ministry Approves Use Of Areplivir Drug For COVID-19 Treatment - UrduPoint

The Russian Health Ministry approved the use of Favipiravir-based drug Areplivir manufactured by pharmaceutical company Promomed for treatment of coronavirus patients, according to information in the state medicines registry.The trade name of the drug is Areplivir. The international...

www.urdupoint.com